The effectiveness of helmets in preventing shrapnel wounds and internal damage due to blast shock waves has been studied. Carbon nanotubes and similar nanostructures have also recently generated heightened interest due to their strength-to-weight ratio and other unique properties. Therefore, to understand and develop a helmet with improved protection, it is necessary to develop computational procedures that will enable the accurate modeling of traumatic head injuries as well as the precise measurement of the mechanical properties of nanostructures and how these characteristics behave when embedded as an advanced composite structure into a helmet. In this study, a multiscale simulation strategy is used to estimate the mechanical characteristics of advanced composite structures with embedded nanostructures. In most of the previous theoretical works, an analysis dedicated to improving the design of the helmet using composite structures was not included due to a lack of understanding of the interactions of the nanostructures with the matrix materials. In this work, the role of the helmet on the over pressurization and impulse experienced by the head during blast shock wave and blunt force trauma due to shrapnel impacts is studied. In addition, the properties of nano-composite structures are estimated using molecular dynamics (MD) simulations and then scaled to the macroscopic level using continuum mechanic formulations. This modeling is further developed using Finite Element (FE) analysis to demonstrate the effectiveness of various types of nanostructures in energy absorption. An analysis is carried out on a model of an unprotected head to compare the results to those obtained when protected by a helmet containing different nanostructures. The developed multiscale model is used to improve the composition of helmets and the general understanding of the effects of blast shock wave and shrapnel impacts thereby leading to the mitigation and prevention of traumatic head injuries.